North Canterbury's Pahau River, situated in one of the most intensively irrigated catchments in the country, has been awarded the supreme prize for most improved river at the annual River Awards.

The top prize was based on the Hurunui river showing the most declining levels of the bacteria E coli over the last 10 years, achieving reductions of 15.6 per cent a year.

Pahau Enhancement Group chairman and dairy farmer David Croft said the result came as no surprise.

"The farming community has been aware of problems with the Pahau for more than 10 years and that's why the enhancement group was originally set up – because of poor water quality. We had a choice to deal with it or ECan (Environment Canterbury) would take the initiative," Croft said.

Cawthron Foundation chairman Dr Morgan Williams said a shift to more precise irrigation and better management practices had brought about the improvement.

Second prize nationally for most improved river was awarded to the Waingawa River in Wairarapa, and third went to the Wairoa River which drains the Hunua catchment south of Auckland.

Besides the three national winners, the judges awarded the most improved in each region: Hakaru River (Northland), Waitekauri River (Waikato), Omanawa River (Bay of Plenty), Punehu Stream (Taranaki), Whangaehu River (Horizons), Orphanage Stream (Nelson), Aparima River (Southland).

This year the rivers were judged solely on levels of E coli; each year the prize organisers select a different indicator for assessing improving water so one year it may be nitrogen, the next phosphorus.

Border dyke irrigation, which used to lead to polluting run-off, is now a thing of the past for farmers operating alongside the Pahau River.

But while the Pahau's E coli levels are low, the same cannot be said for nitrogen, for which it is rated among the worst 25 per cent in the country, or clarity, for which it is in the worst 50 per cent.

Nevertheless Croft said there had been a "definite downward trend" for nitrogen and phosphorus over the last five years.

It was not assessed for swimmability as regional council ECan did not monitor that factor.

The Pahau passes through farmland within the Hurunui catchment, and is swelled by spring-fed waterways that are also on farms.

Any change to water quality had to be made by farmers.

Key to the improved E coli levels was a change to the way in which irrigated water was spread throughout farms.

When the scheme was developed in the 1970s, it used a low-cost border dyke system, using gravity rather than pumping.

The downside was that by-wash – the leftover water that drains into waterways taking sediment and phosphorous with it – polluted the river that ran through much of the dairy farming area.

Border dykes were now a feature of the past, said Amuri Irrigation Company, which manages the investment on behalf of about 130 shareholders and irrigates 28,000 hectares.

"They have spent a significant amount of money, we've just invested $80 million in a pipe upgrade so there will be no more border dyke irrigation in the catchment, the last farm has been compelled to shift to a more efficient spray irrigation," general manager Andrew Barton said.

Farmers face a bill of between $5000 to $7000 per hectare to put in centre pivot spray irrigators.

In 2000, total irrigated area in the Amuri was about 18,000ha and all but 15 farmers used a border dyke system.

Irrigation was initially seen as an insurance tool against extreme weather but is now used as a management tool to gain maximum productivity, as well as to improve water quality.

Judges Professor Gillian Lewis of the University of Auckland), Dr Roger Young of the Cawthron Institute, and Dr Clive Howard-Williams of Niwa said they assessed the strength and significance of trends in the data using a statistical test called the Seasonal Mann Kendall Trend Test.

From an initial database of 536 sites, they found 49 river sites with strong evidence of improving trends in E coli concentrations.

They then consulted regional councils and other groups to ensure changes in land management and restoration initiatives had brought about the improvements.

Rivers were considered for a national award if water sampling had been done monthly for 10 years.

E coli is a type of bacteria commonly found in the intestines of warm-blooded mammals, including people and birds. It is often associated with intensive dairying and while not generally life threatening, can lead to more serious diseases such as giardia or hepatitis A.

The awards are run by Cawthron Foundation, with support provided by the Gawith-Deans family trust, Living Water, Tourism Holdings, Ministry for Environment and the Department of Conservation.